Mercurial > repos > brinkmanlab > mauve_contig_mover
diff mcm_stitch.xml @ 0:c14690ec0c9f draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author | brinkmanlab |
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date | Fri, 24 Jan 2020 17:43:19 -0500 |
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children | 1e2b70ac2ad6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mcm_stitch.xml Fri Jan 24 17:43:19 2020 -0500 @@ -0,0 +1,53 @@ +<tool id="mauve-contig-mover-stitch" name="Mauve Contig Mover - Stitch" version="1.0" profile="16.04"> + <description>Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates</description> + <edam_topics> + <edam_topic>topic_0196</edam_topic> + <edam_topic>topic_0091</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3436</edam_operation> + <edam_operation>operation_0232</edam_operation> + </edam_operations> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.73">biopython</requirement> + </requirements> + <version_command><![CDATA[ $__tool_directory__/stitch.py -v ]]></version_command> + <command detect_errors="aggressive"><![CDATA[ + python $__tool_directory__/stitch.py + #if $seqid + -s '$seqid' + #else + -s '$draft.element_identifier.replace(" ", "_")' + #end if + $pad_len $draft $draft.ext + #if $contigs + $contigs + #end if + > $output + ]]></command> + <inputs> + <param name="draft" type="data" format="abi,abi-trim,ace,cif-atom,cif-seqres,clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,ig,imgt,nexus,pdb-seqres,pdb-atom,phd,phylip,pir,seqxml,sff,sff-trim,stockholm,swiss,tab,qual,uniprot-xml,gff3" label="Draft" /> + <param name="contigs" type="data" format="tabular" label="Contigs" optional="true" help="Contigs output from Mauve Contig Mover" /> + <param name="pad_len" type="integer" min="0" value="1000" label="Pad length" help="Specify the length of padding to put between contigs" /> + <param name="seqid" type="text" value="" label="Stitched sequence ID" help="Specify an ID to use for the stitched record, the dataset ID is used otherwise" /> + </inputs> + <outputs> + <data name="output" format_source="draft" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="draft" value="test-data/draft_bioperl.gbff" ftype="genbank" /> + <param name="contigs" value="test-data/contig_order.tabular" ftype="tabular" /> + <output name="output" checksum="sha256:08afe06a0f1eb96aa7f2a5b9e8a5ca15a4775c884f3144b6d82f2a0668cdb210" ftype="genbank" /> + </test> + </tests> + <help><![CDATA[ + Stitch contigs into a single contig. + Compliments reversed sequences and rewrites all feature coordinates. + For gankbank and embl, 'source' features are combined. + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.3364789</citation> + </citations> +</tool>